|
| Status |
Public on Sep 16, 2011 |
| Title |
MCF-7 cell_DMSO_12hr_biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
MCF-7_DMSO
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
cell type: Breast Cancer Cells
|
| Treatment protocol |
MCF-7 cells were treated with DMSO vehicle, tRA, or tRA/H for 12 hours
|
| Growth protocol |
MCF-7 human breast cancer cells were maintained in a 1:1 ratio of DMEM and Ham’s F-12 media (Gibco), 10% FBS (Invitrogen) and 1% penicillin/streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent (Invitrogen) and chloroform (Sigma). RNA integrity and quantity were determined by the Agilent Bioanalyzer 2100 by the MicroArray Shared Resource (MASR) for the OSU Comprehensive Cancer Center (OSUCCC).
|
| Label |
Biotin
|
| Label protocol |
Biotinylated-cRNA was generated from 2 ug of RNA according to the manufacturer’s protocol in the Affymetrix GeneChip® Expression Analysis Technical Manual.
|
| |
|
| Hybridization protocol |
15ug of labeled and fragmented cRNA was hybridized at 45 C for 16 hours at 60rpm. GeneChips were washed and stained on the Affymetrix Fluidics Station 450 according to Affymetrix protocol.
|
| Scan protocol |
Raw data was generated with Affymetrix GeneChip Operating Software on a Human Genome U133 plus 2.0 Affymetrix platform. Briefly, gene chips were scanned with the Affymetrix GeneChip Scanner 3000 7G for data generation and Affymetrix AGCC software and Expression Console was used for data processing.
|
| Description |
MCF-7_DMSO_2
|
| Data processing |
Background correction and normalization was performed and gene expression level was summarized over probes using the RMA method. A filtering method based on the percentage of samples with expression value above noise level was applied to filter out probe-sets with little or no expression. Generalized linear models were used to detect differentially expressed genes between DMSO-, tRA- or tRA/H-treated MCF-7 cells. In order to improve the estimates of variability and statistical tests for differential expression, a variance shrinkage method was employed. The differentially expressed genes were claimed based on the p-values by controlling the average number of false positives at 1 over all the tested probe sets. Fold changes of at least 1.5 were used to further reduce the list of significant probe-sets after controlling the number of false positives.
|
| |
|
| Submission date |
Sep 15, 2011 |
| Last update date |
Sep 16, 2011 |
| Contact name |
Sissy Jhiang |
| E-mail(s) |
[email protected]
|
| Phone |
614-292-4312
|
| Organization name |
The Ohio State University
|
| Department |
Physiology and Cell Biology
|
| Street address |
1645 Neil Ave
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE32161 |
Microarray analysis of genes associated with cell surface NIS protein levels in breast cancer |
|
